+Open data
-Basic information
Entry | Database: PDB / ID: 7ufs | |||||||||
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Title | Cryo-EM Structure of Bl_Man38B at 3.4 A | |||||||||
Components | Alpha-mannosidase | |||||||||
Keywords | HYDROLASE / n-glycan / probiotic / a-mannosidase / gh38 | |||||||||
Function / homology | Function and homology information alpha-mannosidase activity / mannose metabolic process / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bifidobacterium longum (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Santos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Cryo-EM Structure of Bl_Man38B at 3.4 A Authors: Santos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ufs.cif.gz | 712.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ufs.ent.gz | 577.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ufs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ufs_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7ufs_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7ufs_validation.xml.gz | 106.9 KB | Display | |
Data in CIF | 7ufs_validation.cif.gz | 160.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7ufs ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7ufs | HTTPS FTP |
-Related structure data
Related structure data | 26479MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 118789.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: NCC 2705 / Gene: GBC45_07040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L4U5G4 #2: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetramer of Bl_Man38B / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.475 MDa / Experimental value: NO |
Source (natural) | Organism: Bifidobacterium longum (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5 |
Specimen | Conc.: 0.783 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 0.01 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7865 / Symmetry type: POINT | |||||||||||||||||||||||||||
Refine LS restraints |
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